This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Three fastq files

Hi I'm trying to download data using the SRA toolkit:

prefetch SRR24516563

and then I used:

fastq-dump SRR24516563 -split-files

The output are three different files SRR24516563_1.fastq, SRR24516563_2.fastq and SRR24516563_3.fastq , this is from a paired end sequencing experiment (single-cell RNA seq), I'm planning to use Cell Ranger to align the reads, my question is: usually the output are 3 files, how do I knew which files should I use ? Should I use files _1 and _2 ?

thanks

fastq sra cellranger
• 2,313 views • link
updated by swbarnes2 swbarnes2 • written by charms.charms • charms.charms

1 answer

It's very simple here by looking at the reads:

  • _1 is only few bp so it must be the index => ignore it
  • _2 is 28bp so it must be R1 with CB/UMI
  • _3 is 91 so that is R2 with the gene expression
• 0 views • link
written by ATpoint ATpoint

This is a very naive question, since I'm new with this type of data, but how are able to tell the reads number, I tried looking at SRA webpage, but wasn't able to get further details.

thanks again

• 0 views • link
written by charms.charms • charms.charms

What do you mean by "reads number"? ATPoint is using their knowledge of single cell RNA-seq and read lengths to deduce which files you need to use.

• 0 views • link
written by Ram Ram

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.

upvote_bookmark_accept

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this